[](https://opensource.org/licenses/MIT)
[](https://codecov.io/gh/Clinical-Genomics/crunchy)
[](https://www.codefactor.io/repository/github/clinical-genomics/crunchy)
# Crunchy
A python wrapper around [spring][spring] and cram (samtools) to compress fastq to spring and bam to cram. When compressing fastqs to spring an integrity check can be performed by using flag: `crunchy compress spring --spring-path <springfile> --first <read_1.fastq> --second <read_2.fastq> --check-integrity`
## Install
### Pip
```
pip install crunchy
```
### Docker
This will install crunchy as well as samtools and spring within the container.
```
docker pull clinicalgenomics/crunchy:0.5
```
Run crunchy using:
```
docker run clinicalgenomics/crunchy:0.5 crunchy
```
### Developers
```
git clone https://github.com/Clinical-Genomics/crunchy
pip install -e .
crunchy --help
Usage: crunchy [OPTIONS] COMMAND [ARGS]...
Base command for crunchy
.---. .---.
: : o : me want cookie!
_..-: o : :-.._ /
.-'' ' `---' `---' " ``-.
.' " ' " . " . ' " `.
: '.---.,,.,...,.,.,.,..---. ' ;
`. " `. .' " .'
`. '`. .' ' .'
`. `-._ _.-' " .' .----.
`. " '"--...--"' . ' .' .' o `.
.'`-._' " . " _.-'`. : o :
.' ```--.....--''' ' `:_ o :
.' " ' " " ; `.;";";";'
; ' " ' . ; .' ; ; ;
; ' ' ' " .' .-'
' " " ' " " _.-'
Options:
--spring-binary TEXT Path to spring binary [default: spring]
--samtools-binary TEXT Path to spring binary [default: samtools]
-t, --threads INTEGER Number of threads to use for spring
compression [default: 8]
-r, --reference TEXT Path to reference genome
--log-level [DEBUG|INFO|WARNING]
Choose what log messages to show
--tmp-dir TEXT If specific temp dir should be used
--help Show this message and exit.
Commands:
auto Run whole pipeline by compressing, comparing and deleting...
compare Compare two files by generating checksums.
compress Compress genomic files
decompress Decompress genomic files
```
## Workflow
Each command can be run separately. To compress all fastq pairs below a directory run `crunchy auto spring <path_to_dir>`.
1. **Recursively find all fastq pairs**
1. **Compress all pairs with spring**
```file_1.fastq + file_2.fastq (spring)-> file.spring```
1. **Decompress with spring**
```file.spring (spring)-> file_1.spring.fastq + file_2.spring.fastq```
1. **Compare checksum with previous**
```file_1.spring.fastq + file_1.fastq (hashlib)-> compare```
1. **Delete fastq** (If the compression was lossless)
```file_1.fastq + file_2.fastq (rm)->```
[spring]: https://github.com/shubhamchandak94/Spring
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